The effects of nanoparticle morphology, especially size and shape, on their interactions with cells are of great interest in understanding the fate of nanoparticles in biological systems and designing them for biomedical applications. While size and shape-dependent cell behavior, endocytosis mechanism, and subcellular distribution of nanoparticles have been investigated extensively with gold and other nanoparticles, studies on iron oxide nanoparticles (IONP), one of the most promising and well-thought-of nanomaterials in biomedical applications, were limited. In this study, we synthesized oligosaccharide-coated water-soluble iron oxide nanorods (IONR) with different core sizes (nm) and different aspect ratios (i.e., length/width), such as IONR(L) at 140/6 nm and IONR(S) at 50/7 nm as well as spherical IONP (20 nm). We investigated how their sizes and shapes affect uptake mechanisms, localization, and cell viability in different cell lines. The results of transmission electron microscopy (TEM) and confocal fluorescence microscopic imaging confirmed the internalization of these nanoparticles in different types of cells and subsequent accumulation in the subcellular compartments, such as the endosomes, and into the cytosol. Specifically, IONR(L) exhibited the highest cellular uptake compared to IONR(S) and spherical IONP, 1.36-fold and 1.17-fold higher than that of spherical IONP in macrophages and pediatric brain tumor medulloblastoma cells, respectively. To examine the cellular uptake mechanisms preferred by the different IONR and IONP, we used different endocytosis inhibitors to block specific cellular internalization pathways when cells were treated with different nanoparticles. The results from these blocking experiments showed that IONR(L) enter macrophages and normal kidney cells through clathrin-mediated, dynamin-dependent, and macropinocytosis/phagocytosis pathways, while they are internalized in cancer cells primarily via clathrin/caveolae-mediated and phagocytosis mechanisms. Overall, our findings provide new insights into further development of magnetic IONR-based imaging probes and drug delivery systems for biomedical applications.